Dear Simon and Sergei,

I was trying to use the Lineage Dual and Dual model implemented in the Pond and Muse 2005 MBE paper, which allows the dN and dS estimated separately and varies among both branches and sites.
But I cannot figure out what are the settings to use them.
Esp for the lineage dual model, is it implemented in Hyphy 2.0 or 1.0?

If yes, could you please explain to me how to use them, or tell me where can i find the information on commands? Thanks a billion in advance.

Best,
Jingjing